In the first place, we would like to stress that Istikharah prayer is a two-rak`ah non-obligatory Prayer by which one seeks Allah’s guidance when he is confused or can’t choose between permissible alternatives. In this case, the Muslim should pray to Allah the Almighty to guide him to whatever He sees fit for him and make his heart satisfied with the decision.
In the Prayer, one asks Allah to facilitate the matter if it is good and turn it away if it is not. Thus, after praying Istikharah, one should decide on a course of action, and trust that if the matter does not work out, it is because it was not good for him. One should not then feel disappointed if things did not go as hoped.
Istikharah is only prescribed for matters deemed permissible by the Shari`ah and not for any issue that plainly opposes Allah’s Laws. It is when you have two permissible options and you do not know which is better for you that you should resort to Allah the Almighty to seek His guidance. Moreover, we should stress here that there is nothing wrong with performing istikharah after witr.
Sheikh Muhammad Nur Abdullah, ISNA President and Member of the Fiqh Council of North America, states the following: “There are lots of misconceptions about istikharah prayer. Some people think we should make it at the end of the night; some say you have to go to sleep after; some say you must see a dream, etc. All these claims are baseless and find no support from the Qur’an and the Sunnah.
the Prophet (peace and blessings be upon him) commanded us to perform two non-obligatory raka’ahs and then pray with the authentic du’a’ of istikharah. This means the du’a’ will be said upon finishing the Salah, so how can we then stop talking. Since he—the Prophet—said offer two rak’ahs and did not specify the time, then no body has this authority to add this stipulation. Istikharah, therefore, can be offered any time in the day and we can freely talk after the prayer. If we are still hesitant and cannot decide the decision of Allah, we can repeat it till we receive guidance.”